Journal Article

Accelerating Multiple Sequence Alignment with the Cell BE Processor

Hans Vandierendonck, Sean Rul and Koen De Bosschere

in The Computer Journal

Published on behalf of British Computer Society

Volume 53, issue 6, pages 814-826
Published in print July 2010 | ISSN: 0010-4620
Published online September 2009 | e-ISSN: 1460-2067 | DOI:
Accelerating Multiple Sequence Alignment with the Cell BE Processor

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The Cell Broadband Engine (BE) Architecture is a new heterogeneous multi-core architecture targeted at compute-intensive workloads. The architecture of the Cell BE has several features that are unique in high-performance general-purpose processors, most notably the extensive support for vectorization, scratch pad memories and explicit programming of direct memory accesses (DMAs) and mailbox communication. While these features strongly increase programming complexity, it is generally claimed that significant speedups can be obtained by using Cell BE processors. This paper presents our experiences with using the Cell BE architecture to accelerate Clustal W, a bio-informatics program for multiple sequence alignment. We report on how we apply the unique features of the Cell BE to Clustal W and how important each is in obtaining high performance. By making extensive use of vectorization and by parallelizing the application across all cores, we demonstrate a speedup of 24.4 times when using 16 synergistic processor units on a QS21 Cell Blade compared to single-thread execution on the power processing unit. As the Cell BE exploits a large number of slim cores, our highly optimized implementation is just 3.8 times faster than a 3-thread version running on an Intel Core2 Duo, as the latter processor exploits a small number of fat cores.

Keywords: bio-informatics; cell broadband engine; parallelization

Journal Article.  0 words. 

Subjects: Computer Science

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